I believe that usually these internal Xcode errors are triggered by -[NSException raise] in the source code. You may be able to set a breakpoint (yes, with gdb attached to Xcode) and gather clues. I admit this is a somewhat gallant effort to ask of a developer, but if you're curious and really determined not to lose your project and start from scratch, it may be your only choice.
I have used a combination of gdb debugging and manual editing of project files to repair situations like this before. Best of course is if you have a backup copy of the project file before the corruption occurred. You might find my blog entry on the subject of debugging an Xcode error dialog:
http://www.red-sweater.com/blog/67/xcode-search-gone-mad
Either inspiring or discouraging :)
